In what order is electronic baffle on Quickdraw resolved during end phase?
Does First Player remove his token first or is that done automatically for both players at the end of the end phase?

In case of a timing conflict without there being another specification (i.e. for system, activation, engagement), first player does all of their stuff at that timing, then second player does all of their stuff at that timing.

there is no restriction, it's all during the end phase, so everything is done in player order. the first player resolves all effects, such as removing tokens or triggering other abilities that happen during the end phase, then the second player does the same thing.

being the second player is very beneficial for this interaction because the first player removes all of his tokens before you get the opportunity to trigger electronic baffle, which you can choose to do before removing your own tokens, since it's your own effect.